: Perhaps in the High Charity network Cortana learned enough about Flood
: physiology to thoerize that she might be able to use it/them as a network
: to live in, even use them to stop the Covies and the Flood.

There's a rather large hole in this philosophy that you seem to have, and that is the fact that the Covenant themselves know next to nothing about the flood. Such is to say that Cortana would learn next to nothing from High Charity's network. High Charity is just a covenant mobile planet, with the exception of the Forerunner relic Truth escapes on, its all stolen technology (The ship may very well be stolen as well, who knows.). The only place she could get true information about the flood would be the Forerunner databases, so perhaps she learned this while on Beta Halo? Mayhaps, who knows.